Background Chromosome conformation capture-based methods, especially Hi-C, enable scientists to detect genome-wide chromatin interactions and study the spatial organization of chromatin, which plays important roles in gene expression regulation, DNA replication and repair etc. Thus, developing computational methods to unravel patterns behind the data becomes critical. Existing computational methods focus on intrachromosomal interactions and ignore interchromosomal interactions partly because there is no prior knowledge for interchromosomal interactions and the frequency of interchromosomal interactions is much lower while the search space is much larger. With the development of single-cell technologies, the advent of single-cell Hi-C makes interrogating the spatial structure of chromatin at single-cell resolution possible. It also brings a new type of frequency information, the number of single cells with chromatin interactions between two disjoint chromosome regions. Results Considering the lack of computational methods on interchromosomal interactions and the unsurprisingly frequent intrachromosomal interactions along the diagonal of a chromatin contact map, we propose a computational method dedicated to analyzing interchromosomal interactions of single-cell Hi-C with this new frequency information. To the best of our knowledge, our proposed tool is the first to identify regions with statistically frequent interchromosomal interactions at single-cell resolution. We demonstrate that the tool utilizing networks and binomial statistical tests can identify interesting structural regions through visualization, comparison and enrichment analysis and it also supports different configurations to provide users with flexibility. Conclusions It will be a useful tool for analyzing single-cell Hi-C interchromosomal interactions.
Comparing with natural imaging datasets used in transfer learning, the effects of med- ical pre-training datasets are underexplored. In this study, we carry out transfer learning pre-training dataset effect analysis in breast cancer imaging by evaluating three popular deep neural networks and one patch-based convolutional neural network on three target datasets under different fine-tuning configurations. Through a series of comparisons, we conclude that the pre-training dataset, DDSM, is effective on two other mammogram datasets. However, it is ineffective on an ultrasound dataset. What is more, fine-tuning may mask the inefficacy of a pre-training dataset. In addition, the efficacy/inefficacy of DDSM on the target datasets is corroborated by a representational analysis. At last, we show that hybrid transfer learning cannot mitigate the masking effect of fine-tuning.
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